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Computational Nature of Gene Assembly in Ciliates

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Handbook of Natural Computing

Abstract

Ciliates are a very diverse and ancient group of unicellular eukaryotic organisms. A feature that is essentially unique to ciliates is the nuclear dualism, meaning that they have two functionally different types of nuclei, the macronucleus and the micronucleus. During sexual reproduction a micronucleus is transformed into a macronucleus – this process is called gene assembly, and it is the most involved naturally occurring example of DNA processing that is known to us. Gene assembly is a fascinating research topic from both the biological and the computational points of view.

In this chapter, several approaches to the computational study of gene assembly are considered. This chapter is self-contained in the sense that the basic biology of gene assembly as well as mathematical preliminaries are introduced. Two of the most studied molecular models for gene assembly, intermolecular and intramolecular, are presented and the main mathematical approaches used in studying these models are discussed. The topics discussed in more detail include the string and graph rewriting models, invariant properties, template-based DNA recombination, and topology-based models. This chapter concludes with a brief discussion of a number of research topics that, because of the space restrictions, could not be covered in this chapter.

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Acknowledgments

MD and GR acknowledge support by NSF, grant 0622112. IP acknowledges support by the Academy of Finland, grants 108421 and 203667. NJ has been supported in part by the NSF grants CCF 0523928 and CCF 0726396.

Author information

Authors and Affiliations

  1. Leiden Institute of Advanced Computer Science, Universiteit Leiden, Leiden, The Netherlands

    Robert Brijder & Grzegorz Rozenberg

  2. Departments of Computer Science and Biology, University of Western Ontario, London, Ontario, Canada

    Mark Daley

  3. Department of Mathematics, University of Turku, Turku, Finland

    Tero Harju

  4. Department of Mathematics, University of South Florida, Tampa, FL, USA

    Nataša Jonoska

  5. Department of Information Technologies, Åbo Akademi University, Turku, Finland

    Ion Petre

  6. Department of Computer Science, University of Colorado, Boulder, CO, USA

    Grzegorz Rozenberg

Authors
  1. Robert Brijder
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  2. Mark Daley
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  3. Tero Harju
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  4. Nataša Jonoska
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  5. Ion Petre
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  6. Grzegorz Rozenberg
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Editor information

Editors and Affiliations

  1. LIACS, Leiden University, Leiden, The Netherlands

    Grzegorz Rozenberg

  2. Computer Science Department, University of Colorado, Boulder, USA

    Grzegorz Rozenberg

  3. LIACS, Leiden University, Leiden, The Netherlands

    Thomas Bäck

  4. LIACS, Leiden University, Leiden, The Netherlands

    Joost N. Kok

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Brijder, R., Daley, M., Harju, T., Jonoska, N., Petre, I., Rozenberg, G. (2012). Computational Nature of Gene Assembly in Ciliates. In: Rozenberg, G., Bäck, T., Kok, J.N. (eds) Handbook of Natural Computing. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-92910-9_37

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